annotate README @ 6:091154194ce8 draft

Uploaded
author devteam
date Wed, 12 Feb 2014 16:32:16 -0500
parents 75b252cf390e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
75b252cf390e Uploaded
devteam
parents:
diff changeset
1 ANNOVAR needs to be installed manually in the following way:
75b252cf390e Uploaded
devteam
parents:
diff changeset
2
75b252cf390e Uploaded
devteam
parents:
diff changeset
3 1a) If you already have ANNOVAR installed on your system, simply edit the tool-data/annovar.loc file to reflect locations of
75b252cf390e Uploaded
devteam
parents:
diff changeset
4 the perl scripts (annotate_variation.pl and convert2annovar.pl) and humandb directory (directory containing the annovar database files)
75b252cf390e Uploaded
devteam
parents:
diff changeset
5
75b252cf390e Uploaded
devteam
parents:
diff changeset
6 1b) If you do not have ANNOVAR installed, request annovar download and sign license here:
75b252cf390e Uploaded
devteam
parents:
diff changeset
7 http://www.openbioinformatics.org/annovar/annovar_download_form.php
75b252cf390e Uploaded
devteam
parents:
diff changeset
8
75b252cf390e Uploaded
devteam
parents:
diff changeset
9 i) Once downloaded, install annovar per the installation instructions and note the installation path.
75b252cf390e Uploaded
devteam
parents:
diff changeset
10
75b252cf390e Uploaded
devteam
parents:
diff changeset
11 ii) Then download all desired databases for all desired builds as follows:
75b252cf390e Uploaded
devteam
parents:
diff changeset
12 annotate_variation.pl -downdb -buildver <build> [-webfrom annovar] <database> <humandb>
75b252cf390e Uploaded
devteam
parents:
diff changeset
13
75b252cf390e Uploaded
devteam
parents:
diff changeset
14 where <humandb> is location where all database files should be stored
75b252cf390e Uploaded
devteam
parents:
diff changeset
15 and <database> is the database file to download, e.g. refGene (see bottom of document for all available database files at the time of writing this tool)
75b252cf390e Uploaded
devteam
parents:
diff changeset
16 and <build> can be hg18 or hg19 for humans, also other organisms available.
75b252cf390e Uploaded
devteam
parents:
diff changeset
17
75b252cf390e Uploaded
devteam
parents:
diff changeset
18 list of all available databases can be found here: http://www.openbioinformatics.org/annovar/annovar_db.html
75b252cf390e Uploaded
devteam
parents:
diff changeset
19
75b252cf390e Uploaded
devteam
parents:
diff changeset
20 iii) edit the tool-data/annovar.loc file to reflect location of humandb folder
75b252cf390e Uploaded
devteam
parents:
diff changeset
21
75b252cf390e Uploaded
devteam
parents:
diff changeset
22 2) add the annovar scripts convert2annovar.pl and table_annovar.pl to your Galaxy user's path
75b252cf390e Uploaded
devteam
parents:
diff changeset
23
75b252cf390e Uploaded
devteam
parents:
diff changeset
24 3) restart galaxy instance for changes in .loc file to take effect